MolNFT v1 · #126280 · protein

Structure of the minimal RBM7 - ZCCHC8 complex

5LXY · RNA-binding protein 7: “Structure of the minimal RBM7 - ZCCHC8 complex”. X-ray diffraction, 1 ligand (BR), 7 pockets (best druggability 0.76). MolNFT v1 #126280 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5LXY
Type: protein
Length: 784 residues
Chains: 14
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA-binding protein 7; Zinc finger cchc domain-containing protein 8
UniProt: Q9Y580, Q6NZY4
Ligands: BR
Pockets: 7 · best druggability 0.76

Structure

x-ray diffraction · 11 distinct chains · 30% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RNA-binding protein 7	protein	78	23% helix, 29% strand	Q9Y580
D, C	Zinc finger cchc domain-containing protein 8	protein	39	46% helix, 0% strand	Q6NZY4
B	RNA-binding protein 7	protein	76	28% helix, 30% strand	Q9Y580
E	RNA-binding protein 7	protein	73	23% helix, 32% strand	Q9Y580
F, H	Zinc finger cchc domain-containing protein 8	protein	40	45% helix, 3% strand	Q6NZY4
G	RNA-binding protein 7	protein	72	24% helix, 32% strand	Q9Y580
I	RNA-binding protein 7	protein	79	25% helix, 25% strand	Q9Y580
J, L	Zinc finger cchc domain-containing protein 8	protein	38	45% helix, 0% strand	Q6NZY4
K	RNA-binding protein 7	protein	71	24% helix, 32% strand	Q9Y580
M	RNA-binding protein 7	protein	64	27% helix, 27% strand	Q9Y580
N	Zinc finger cchc domain-containing protein 8	protein	37	46% helix, 0% strand	Q6NZY4

Ligands and binding sites

BR · Bromide ion · ion · 9 copies · chains D, C, B, F, G, H, J, L, N

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	452	0.76	0.85	66	BR
2	118	0.57	0.84	26	empty
3	111	0.56	0.84	25	BR
4	78	0.49	0.83	21	BR
5	100	0.33	0.73	22	empty

Interfaces

25 interfaces between chains.

B–C · 902 Å² buried · 8 hydrogen bonds · protein-protein
E–F · 857 Å² buried · 8 hydrogen bonds · protein-protein
A–D · 842 Å² buried · 10 hydrogen bonds · protein-protein
G–H · 824 Å² buried · 9 hydrogen bonds · protein-protein
I–J · 742 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

5LXY · Structure of the minimal RBM7 - ZCCHC8 Complex · the same entry in another collection · chain K against K, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q9Y580
Every structure of UniProt Q6NZY4
Elsewhere: RCSB PDB 5LXY · PDBe 5LXY · UniProt Q9Y580 · UniProt Q6NZY4

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